from repo2data.repo2data import Repo2Data
import os
import pickle
import matplotlib.pyplot as plt
import chart_studio.plotly as py
import plotly.graph_objs as go
import numpy as np
from plotly import __version__
from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
from IPython.display import display, HTML
from plotly import tools
from contextlib import contextmanager
import sys, os
@contextmanager
def suppress_stdout():
with open(os.devnull, "w") as devnull:
old_stdout = sys.stdout
sys.stdout = devnull
try:
yield
finally:
sys.stdout = old_stdout
with suppress_stdout():
data_req_path = os.path.join("..","..","..", "binder", "data_requirement.json")
repo2data = Repo2Data(data_req_path)
DATA_ROOT = os.path.join(repo2data.install()[0],"t1-book-neurolibre")
filename = os.path.join(DATA_ROOT,"01",'figure_2.pkl')
with open(filename, 'rb') as f:
params, signal_WM, signal_GM, signal_CSF = pickle.load(f)
filename = os.path.join(DATA_ROOT,"01",'figure_3.pkl')
with open(filename, 'rb') as f:
T1_range, signal_T1_Eq1, signal_T1_Eq3 = pickle.load(f)
config={'showLink': False, 'displayModeBar': False}
init_notebook_mode(connected=True)
data1 = [dict(
visible = False,
x = params["TI"],
y = abs(signal_T1_Eq3[ii]),
name = '[Eq. 2.3] – Long TR approximation',
text = '[Eq. 2.3] – Long TR approximation',
hoverinfo = 'x+y+text') for ii in range(len(T1_range))]
data1[3]['visible'] = True
data2 = [dict(
visible = False,
x = params["TI"],
y = abs(signal_T1_Eq1[ii]),
line = dict(
color = ('rgb(22, 96, 167)'),
dash = 'dash'),
name = '[Eq. 2.1] – General Equation',
text = '[Eq. 2.1] – General Equation',
hoverinfo = 'x+y+text') for ii in range(len(T1_range))]
data2[3]['visible'] = True
data = data1 + data2
steps = []
for i in range(len(T1_range)):
step = dict(
method = 'restyle',
args = ['visible', [False] * len(data1)],
label = str(T1_range[i])
)
step['args'][1][i] = True # Toggle i'th trace to "visible"
steps.append(step)
sliders = [dict(
x = 0,
y = -0.0,
active = 3,
currentvalue = {"prefix": "T<sub>1</sub> value (s): <b>"},
pad = {"t": 50, "b": 10},
steps = steps
)]
layout = go.Layout(
width=580,
height=400,
margin=go.layout.Margin(
l=80,
r=40,
b=60,
t=10,
),
annotations=[
dict(
x=0.5004254919715793,
y=-0.2,
showarrow=False,
text='Inversion Time – TI (ms)',
font=dict(
family='Times New Roman',
size=22
),
xref='paper',
yref='paper'
),
dict(
x=-0.14,
y=0.5,
showarrow=False,
text='Signal (magnitude)',
font=dict(
family='Times New Roman',
size=22
),
textangle=-90,
xref='paper',
yref='paper'
),
],
xaxis=dict(
autorange=False,
range=[0, 5],
showgrid=False,
linecolor='black',
linewidth=2
),
yaxis=dict(
autorange=False,
range=[0, 1],
showgrid=False,
linecolor='black',
linewidth=2
),
legend=dict(
x=0.5,
y=0.5,
traceorder='normal',
font=dict(
family='Times New Roman',
size=12,
color='#000'
),
bordercolor='#000000',
borderwidth=2
),
sliders=sliders,
plot_bgcolor='white'
)
fig = dict(data=data, layout=layout)
iplot(fig, filename = 'ir_fig_3.html', config = config)
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